Interaction of polyamines with fragments and whole molecules of yeast phenylalanine-specific transfer RNA

Effects of polyamines on DNA synthesis using various subcellular DNA polymerases extracted from normal rat liver, tumour-bearing rat liver, and tumour cells

The effects of polyamines on DNA synthesis in vitro using various subcellular DNA polymerase fractions from normal and tumour-bearing rat livers, and tumour cells were investigated. When nuclear and mitochondrial DNA polymerase fractions were used, DNA synthesis on activated DNA was increased 3.5-8-fold by the addition of 20 mM putrescine or cadaverine. However, DNA synthesis was not stimulated by the addition of spermidine or spermine at any concentration tested. In contrast, DNA synthesis using the cytoplasmic DNA polymerase fraction was not stimulated at various concentrations of any of the four polyamines tested. The stimulatory effects of putrescine and cadaverine were absent when nuclear fractions from tumour-bearing rat liver or from tumour cells were used. In addition, in vitro DNA synthesis was not stimulated by 20 mM putrescine or cadaverine when nuclear extracts from the livers of rats administered putrescine subcutaneously were used. The specific activities of DNA polymerases extracted from tumour cells and tumour-bearing rat liver were already fully stimulated. These results suggest that DNA polymerases in tumour cells and tumour-bearing liver cells are stimulated by trapped putrescine produced in tumour cells and are thus no longer activated by exogenous putrescine.

Photoaffinity polyamines: interactions with AcPhe-tRNA free in solution or bound at the P-site of Escherichia coli ribosomes

Two photoreactive derivatives of spermine, azidobenzamidino (ABA)-spermine and azidonitrobenzoyl (ANB)-spermine, were used for mapping of polyamine binding sites in AcPhe-tRNA free in solution or bound at the P-site of Escherichia coli poly(U)-programmed ribosomes. Partial nuclease digestion indicated that the deep pocket formed by nucleosides of the D-stem and the variable loop, as well as the anticodon stem, are preferable polyamine binding sites for AcPhe-tRNA in the free state. ABA-spermine was a stronger cross-linker than ANB-spermine. Both photoprobes were linked to AcPhe-tRNA with higher affinity when the latter was non-enzymatically bound to poly(U)-programmed ribosomes. In particular, the cross-linking at the TpsiC stem and acceptor stem was substantially promoted. The photolabeled AcPhe-tRNA.poly(U).ribosome complex exhibited moderate reactivity towards puromycin. The attachment of photoprobes to AcPhe-tRNA was mainly responsible for this defect. A more complicated situation was revealed when the AcPhe-tRNA.poly(U).ribosome complex was formed in the presence of translation factors; the reactivity towards puromycin was stimulated by irradiating such a complex in the presence of photoprobes at 50 microM, with higher concentrations being inhibitory. The stimulatory effect was closely related with the binding of photoprobes to ribosomes. The results are discussed on the basis of possible AcPhe-tRNA conformational changes induced by the incorporation of photoprobes.

On the roles of magnesium and spermidine in the isoleucyl-tRNA synthetase reaction. Analysis of the reaction mechanism by total rate equations

The reaction of isoleucyl-tRNA synthetase from Escherichia coli B was analysed by deriving total steady-state rate equations for the ATP/PPi exchange reaction and for the aminoacylation of tRNA, and by fitting these rate equations to series of experimental results. The analysis suggests that (a) a Mg2+ inhibits the aminoacylation of tRNA but not the activation of the amino acid. In the chosen mechanism, this enzyme-bound Mg2+ is required at the activation step. (b) Another Mg2+ is required at ATP, but the MgATP apparently can be replaced by the spermidine.ATP complex. Spermidine.ATP is a weaker substrate. The role of spermidine.ATP is especially suggested by the relative rates of the aminoacylation of tRNA when the spermidine and magnesium concentrations are varied. The aminoacylation measurements still suggest that (c) two (or more) Mg2+ are bound to the tRNA molecule and are required for enzyme activity at the transfer step, and that these Mg2+ can be replaced by spermidines.

Spermine stimulates the threonyl-tRNA formation in rat liver

The effects of spermine have been studied on the aminoacylation reaction catalyzed by rat liver threonyl-tRNA synthetase. Spermine can not replace Mg2+ in this reaction. However, a stimulatory and synergistic effect was observed on the threonyl-tRNA formation, in the presence of spermine and suboptimal concentration of Mg2+. Other divalent cations like Ba2+, Ca2+, Mn2+ and Co2+ can substitute Mg2+ in the threonyl-tRNA formation, but in all these cases spermine had no significant effect. Spermine prevented the inhibitory effects caused by excess of ATP or tRNA on the aminoacylation reaction. Association constants were determined by equilibrium dialysis for the tRNA-spermine complex (Ka = 3.7 x 10(3) M-1) and by differential spectrophotometry for the ATP-spermine complex (Ka = 7.8 x 10(3) M-1). No enzyme-spermine complex could be detected by equilibrium dialysis. Some roles have been ascribed for the polyamine spermine in the stimulation of the threonyl-tRNA formation. ATP-spermine and tRNA-spermine can not function as substrates for the threonyl-tRNA synthetase, since Mg2+ is indispensable. The stimulatory effect by spermine is important considering the physiological concentration of Mg2+ in the tissues. Probably in vivo spermine would have a relevant role lowering the real Mg2+ concentration required in the aminoacylation reaction.

Effect of zinc ions on tRNA structure. I. Reversed-phase chromatography

The effect of zinc on the chromatographic behavior of four tRNAs was examined on RPC-5 and Aminex A-28 columns. RPC-5 contains dichlorodifluoroethylene beads coated with a quaternary ammonium compound where the substituents are: R1 = methyl, and R2-4 = C8-10 hydrocarbons. Aminex A-28 contains quaternary ammonium covalently attached to styrene-divinylbenzene copolymer lattice and R1-3 are methyl groups. The retentions of tRNAVal, tRNAIle, and tRNALys of E. coli and yeast tRNAPhe on RPC-5 were all markedly increased by Zn2+ ions. In contrast, no increased retention due to Zn2+ was observed when tRNAPhe was chromatographed on Aminex A-28. A model for chromatography on RPC-5 is developed which treats the elution behavior of tRNAs from this matrix as the sum of ion-exchange and hydrophobic interactions. The chromatography of tRNA in the presence and absence of Zn2+ is interpreted in terms of this model and the effects of sodium chloride concentration, temperature, and pH were explored as the experimental variables. These experiments suggest that in the absence of Zn2+ tRNA does not interact appreciably with the hydrophobic surface of the column. The addition of Zn2+ has three effects on chromatography: a decrease in the number of anionic sites on the tRNA which interact with the positively charged ammonium ion, an increase in affinity of the tRNA for these ionic sites, and an increase in affinity of tRNA for hydrophobic sites on the column. All three effects were fully reversed by the addition of Cd2+ (10 mM) or Mg2+ (35 mM), but only partially reversed at lower concentrations of these competing ions. These results show that chromatography on RCP-5 can be a sensitive physical chemical technique for examination of the structure of tRNA, and probably for other nucleic acids as well.

Imino proton NMR assignments and ion-binding studies on Escherichia coli tRNA3Gly

The imino region of the proton NMR spectrum of Escherichia coli tRNA3Gly has been assigned mainly by sequential nuclear Overhauser effects between neighbouring base pairs and by comparison of assignments of other tRNAs. The effects of magnesium, spermine and temperature on the 1H and 31P NMR spectra of this tRNA were studied. Both ions affect resonances close to the G15 . C48 tertiary base pair and in the ribosylthymine loop. The magnesium studies indicate the presence of an altered tRNA conformer at low magnesium concentrations in equilibrium with the high magnesium form. The temperature studies show that the A7 . U66 imino proton (from a secondary base pair) melts before some of the tertiary hydrogen bonds and that the anticodon stem does not melt sequentially from the ends. Correlation of the ion effects in the 1H and 31P NMR spectra has led to the tentative assignment of two 31P resonances not assigned in the comparable 31P NMR spectrum of yeast tRNAPhe. 31P NMR spectra of E. coli tRNA3Gly lack resolved peaks corresponding to peaks C and F in the spectra of E. coli tRNAPhe and yeast tRNAPhe. In the latter tRNAs these peaks have been assigned to phosphate groups in the anticodon loop. Ion binding E. coli tRNA3Gly and E. coli tRNAPhe had different effects on their 1H NMR spectra which may reflect further differences in their charge distribution and conformation.

Influence of the polyamines spermine and spermidine on yeast tRNAPhe as revealed from its imino proton NMR spectrum

A comparison of imino proton NMR spectra of yeast tRNAPhe recorded at various solution conditions indicates, that polyamines have a limited effect on the structure of this tRNA molecule. Polyamines are found to catalyse the solvent exchange of several imino protons in yeast tRNAPhe not only of non hydrogen bonded imino protons, but also of imino protons of the GU and of some AU and tertiary base pairs. It is concluded that at low levels of catalysing components the exchange rates of the latter protons are not determined by the base pair lifetime. In the presence of high levels of spermidine the solvent exchange rates of imino protons of several base pairs in the molecule were assessed as a function of the temperature. Apparent activation energies derived from these rates were found to be less than 80 kJ/mol, which is indicative for (transient) independent opening of the corresponding base pairs. In the acceptor helix the GU base pair acts as a dynamic dislocation. The AU base pairs at one side of the GU base pair exhibit faster transient opening than the GC base pairs on the other side of this wobble pair. The base pairs m2GC10 and GC11 from the D stem and GC28 from the anticodon stem show relatively slow opening up to high temperatures. Model studies suggest that 1-methyladenosine, an element of tRNA itself, catalyses imino proton solvent exchange in a way similar to polyamines.

Determination of the polyamine content of rat heart mitochondria by the use of heparin-sepharose

Heparin-sepharose has been utilized to remove polyamines adsorbed to the cytoplasmic surface of rat heart mitochondria. The results obtained can be summarized as follows: Heparin-sepharose removes 90% of the spermine, 98% of the spermidine, and 98% of the putrescine adsorbed. Polyamine contents of chromatographed mitochondria amount to 2.66 and 0.36 nmol spermine and spermidine, respectively, per mg of mitochondrial protein.

Structural changes of yeast tRNA(Tyr) caused by the binding of divalent ions in the presence of spermine

The existence of specific sites in tRNA for the binding of divalent cations has been seriously questioned by electrostatic considerations [Leroy & Guéron (1979) Biopolymers, 16, 2429-2446]. However, our earlier studies of the binding of Mg2+ and Mn2+ to yeast tRNA(Tyr) have indicated that spermine creates new binding sites for divalent cations [Weygand-Durasević et al. (1977) Biochim. Biophys, Acta, 479, 332-344; Nöthig-Laslo et al. (1981) Eur. J. Biochem. 117, 263-267]. We have now used yeast tRNA(Tyr), spin labeled at the hypermodified purine (i6A-37) in the anticodon loop, to study the effect of spermine on the binding of manganese ions. The presence of eight spermine molecules per tRNA(Tyr) at high ionic strength (0.2 M NaCl, 0.05 M triethanolamine.HCl) and at low temperature (7 degrees C) enhances the binding of manganese to tRNA(Tyr). This effect could not be explained by electrostatic binding. The initial binding of manganese to tRNA(Tyr) affects the motional properties of the spin label indicating a change of the conformation of the anticodon loop. From the absence of the paramagnetic effect of manganese on the ESR spectra of the spin label one can conclude that the first binding site for manganese is at a distance from i6A-37, influencing the spin label motion through a long-range effect. The enhancement of the binding of manganese to tRNA(Tyr) by spermine is lost upon destruction of its specific macromolecular structure and it does not occur in single stranded or in double-stranded polynucleotides. The observed effect can be explained by the binding of Mn2+ to new sites, created by the binding of spermine, which are specific for the macromolecular structure of tRNA.

The influence of spermine on the structural dynamics of yeast tRNAPhe

A tRNAPhe derivative carrying ethidium at position 37 in the anticodon loop has been used to study the effect of spermine on conformational transitions of the tRNA. As previously reported (Ehrenberg, M., Rigler, R. and Wintermeyer, W. (1979) Biochemistry 18, 4588-4599) in the tRNA derivative the ethidium is present in three states (T1-T3) characterized by different fluorescence decay rates. T-jump experiments show two transitions between the states, a fast one (relaxation time 10-100 ms) between T1 and T2, and a slow one (100-1000 ms) between T2 and T3. In the presence of spermine the fast transition shows a negative temperature coefficient indicating the existence of a preequilibrium with a negative reaction enthalpy. Spermine shifts the distribution of states towards T3, as does Mg2+, but the final ratio [T2]/[T1] obtained with spermine is higher than with Mg2+, which we tentatively interpret to mean that spermine stabilizes one particular conformation of the anticodon loop.

Polyamine requirement for efficient translation of amber codons in vivo

Multiplication of several amber mutants of bacteriophage T7 was decreased in two polyamine-deficient mutants of Escherichia coli K-12 carrying amber suppressors, relative to the multiplication of wild type bacteriophage T7 in the same hosts. In contrast the same T7 amber bacteriophages multiplied well in these strains when supplemented with polyamines. The requirement for polyamines for optimal translation of amber codons in vivo was confirmed by showing that infection of polyamine-depleted E. coli with bacteriophage T7 carrying an amber mutation in gene 1 resulted in an increased accumulation of the amber fragment of the gene 1 protein and a decreased accumulation of the full-length gene 1 protein compared with infection of an amine-supplemented culture. These results indicate that one important function of polyamines in vivo is concerned with protein translation and the protein-synthesizing ribosomal complex.

Binding of spermine to tRNATyr stabilizes the conformation of the anticodon loop and creates strong binding sites for divalent cations

Electron spin resonance (ESR) spectra of yeast tRNATyr. spin-labelled in the isopentenyladenosine residue adjacent to the anticodon, were measured as a function of temperature at various spermine/tRNA ratios. The critical temperature, at which a change in the activation energy for spin-label motion takes place, changes abruptly by almost 10 degrees C upon the addition of the fifth spermine molecule/tRNATyr molecule, indicating a marked stabilization of the anticodon region. Scatchard plots for Mn2+ binding to tRNATyr in the presence of spermine do not follow theoretically predicted curves for electrostatic type of interaction, assuming that four negative charges on tRNA are neutralized by each spermine molecule. It was estimated that two to three new binding sites for divalent cations are created upon the binding of spermine to tRNATyr.

On the binding of Mg2+ and Mn2+ to tRNA

In this paper previous binding studies of Mg2+ and Mn2+ ions to tRNA's are reconsidered. Binding data of some representative examples are interpreted including interactions between charges located on the macroion. Both curved and bell-shaped Scatchard plots can be accounted for quantitatively if corrections are made for electrostatic interactions and, if necessary, for the effect of conformational changes on these interactions. It appears that there is no need to invoke more than one class of binding sites on tRNA's, meaning that the experimental binding data can be described using the same intrinsic pK value for all phosphate groups.

Effect of magnesium and polyamines on the structure of yeast tRNAPhe

The effect of magnesium and polyamines (spermine, spermidine, putrescine and cadaverine) on the structure of yeast tRNAPhe has been investigated. It is found that magnesium induces structural changes and stabilizes hydrogen bonds in the temperature range 22--44 degrees C in 0.17 M sodium. The number of Mg2+ which affect tRNA structure increases from 1 +/- 1 at 22 degrees C to 4 +/- 1 at 44 degrees C and the number of additional base pairs formed in the presence of magnesium increases from 1 +/- 1 at 22 degrees C to 4 +/- 1 at 44 degrees C. The spectral changes are more-or-less sequential. The polyamine spermine stabilizes some, but not all, of the structural features stabilized by magnesium at 44 degrees C, and the combination of magnesium and spermine, at low levels, is more effective than either cation alone in stabilizing tRNA structure. Comparison of the effects of spermine, spermidine, putrescine and cadaverine indicates that it is the asymmetric triamine unit which is important in the stabilization. Some spectral changes induced by magnesium can be assigned to stabilization of specific tertiary structure interactions and to alteration of stacking adjacent to U8-A14.

Allosteric interpretation of Mg2+ binding to the denaturable Escherichia coli tRNAGlu2+

The Mg2+ binding properties of the denaturable tRNAGlu2 from E. coli in 0.1 M Na+, pH7, are characterized by equilibrium dialysis. At 34 degrees C, where the native and denatured conformers are in equilibrium, Mg2+ binding is cooperative. By trapping the tRNA completely in the native conformation at 4 degrees C it is shown that native tRNAGlu2 possesses one strong binding site, K1 = 7.5 x 10(4) M-1 and approximately 36 weak sites with K2 = 8.3 x 10(2) M-1. A significantly lower affinity for the denatured conformer is indicated. We show that Mg2+ effects an allosteric transition from the low affinity denatured conformational state to the high affinity native state and develop the appropriate equations to fit the Mg2+ binding data with physically meaningful parameters. Our results also suggest the previously reported cooperative cation binding to tRNA arises from a cation induced conformational change to the native tRNA conformation and does not reflect the inherent Mg2+ binding properties of the native conformer.

Rate of tritium labeling of specific purines in relation to nucleic acid and particularly transfer RNA conformation

The kinetics of the incorporation of tritium into the C-8 positions of purine units in nucleic acids has been studied. The polymers investigated include poly(A), poly(A): poly (U) duplex, a double-stranded viral RNA, tRNA, and DNA. In the random coil state, the kinetics of incorporation of tritium into the purine sites of the polymers are identical with those for the corresponding purine mononucleotides. When the nucleic acids are in their native conformations, however, the purine labeling rates are reduced below that expected for the free mononucleotides. The magnitude of the effect is remarkably dependent upon the particular nucleic acid. For example, at 37 degrees C the purines in double-stranded DNA label at a rate two- to threefold slower than the corresponding mononucleotides, but in a double-stranded viral RNA, a 30- to 40-fold effect is found. The data suggest a strong influence of microscopic helix structure on the rate of tritium incorporation. First-order rate constants for the exchange of tritium into specific purine sites in yeast tRNAPhe were also determined. This was done by partially labeling the nucleic acid in tritiated water, and subsequently removing free and loosely bound tritium. Under conditions where exchange-out does not occur, the nucleic acid was digested with specific nucleases; chromatographic separation then enabled specific activities of purines from specific sites to be obtained. The rate constants for these sites show a large variation. They are markedly reduced for those residues occurring in cloverleaf helical sections and, in certain cases, for those known from crystallographic data to be involved in tertiary interactions. As examples of bases that can participate in tertiary interactions, the crystal structures show A14 and G15 in special base-pairing arrangements. Both purines (A14 and G15) occur in single-stranded sections of the cloverleaf; both show markedly reduced C-8 hydrogen-exchange rates. On the other hand, rate constants for bases and regions known to be on the outside of the moleculesuch as the anticodon loop and the 3' terminusāre perturbed the least. In one instance, a base in the dihydrouridine loop believed to be involved in tertiary interactions, according to crystallographic studies, incorporates tritium as if it were relatively unperburbed by the tRNA structure. The structural interactions of this base may be partially or completely broken at 37 degrees C in solution.

tRNA methyltransferases from rat liver. Differences in response of partially purified enzymes to polyamines and inorganic salts

Three tRNA methyltransferases, purified from rat liver, have been compared for their activity in the presence of various amines and Mg2+. The enzymes differ with respect to the ion which permits maximal activity; they also differ with respect to the concentration of a given ion necessary for maximal activity. The methyltransferase which forms N2-methylguanine in the region between the dihydrouridine loop and the acceptor stem (2mG I), when assayed using purified tRNA as substrate, shows high activity with 3--5 mM sperimidine or 20 mM putrescine and significantly lower rates of methylation with 200--350 mM ammonium acetate or 1--10 mM magnesium acetate. The enzyme responsible for forming N2-methylguanine between the dihydrouridine and anticodon loops (2mG II) works well in the presence of 0.2--0.5 mM spermidine, 10 mM putrescine or 200--300 mM ammonium acetate and shows slightly lower activity with 1 mM magnesium acetate. The optimal conditions for assaying 1-adenine methyltransferase (1mA) with purified tRNAs are either 200--300 mM ammonium acetate or 30 mM putrescine; spermidine is slightly less effective and magnesium acetate permits less than 25% of maximal activity. The addition of 10 mM Mg2+, in combination with polyamines or NH4+, depresses slightly the activity of the guanine methyltransferases but completely abolishes the polyamine or ammonium-stimulated activity of the adenine methyltransferase. When unfractionated (Escherichia coli) tRNA is used as substrate, the concentrations of polyamines required for optimal methyltransferase activity are increased but the patterns of response of the three enzymes do not differ significantly from those obtained with purified tRNA substrates. Based on the studies with these three enzymes, unfractionated tRNA and 40 mM putrescine should provide the most reliable system for detecting methylating activity if the nature of the tRNA methyltransferase is unknown.